stepBLAST: stepBLASTN: Filter Homologous Sequences

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Filters homologous sequences using the BLASTB tool

Usage

stepBLAST(
  x,
  word.size = 11,
  gapopen = 5,
  gapextend = 2,
  penalty = -3,
  reward = 1
)

Arguments

x	An object of class megapteraProj.
word.size	Integer, ...
gapopen	Integer, ...
gapextend	Integer, ...
penalty	Integer, ...
reward	Integer, ...

Details

sseqid	ID of query sequence that gave the lowest E-value
length	Alignment length
mismatch	Alignment length
qstart	Start of alignment in query
qend	End of alignment in query
sstart	Start of alignment in subject
send	End of alignment in subject
qcovs	Percentage of query coverage per subject
pident	Percentage of identical matches
evalue	Expect value
bitscore	Bit score
sstrand	Percentage of identical matches

References

NCBI BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.